Techniques for manipulating matter at the nanometer scale (“nanoscale”) are important for many electronic, chemical and biological purposes (See Li et al., “Ion beam sculpting at nanometer length scales”, Nature, 412: 166-169, 2001). Among such purposes are the desire to more quickly sequence biopolymers such as DNA. Nanopores, both naturally occurring and artificially fabricated, have recently attracted the interest to molecular biologists and biochemists for the purpose of DNA sequencing.
It has been demonstrated that a voltage gradient can drive a biopolymer such as single-stranded DNA (ssDNA) in an aqueous ionic solution through a naturally-occurring transsubstrate channel, or “nanopore,” such as an α-hemolysin pore in a edgeid bilayer. (See Kasianowicz et al., “Characterization of individual polynucleotide molecules using a substrate channel”, Proc. Natl. Acad. Sci. USA, 93: 13770-13773, 1996). The process in which the DNA molecule goes through the pore has been dubbed “translocation”. During the translocation process, the extended biopolymer molecule blocks a substantial portion of the otherwise open nanopore channel. This blockage decreases the ionic electrical current flow occurring through the nanopore in the ionic solution. The passage of a single biopolymer molecule can therefore be monitored by recording the translocation duration and the decrease in current. Many such events occurring sequentially through a single nanopore provide data that can be plotted to yield useful information concerning the structure of the biopolymer molecule. For example, given uniformly controlled translocation conditions, the length of the individual biopolymer can be estimated from the translocation time.
One desire of scientists is that the individual monomers of the biopolymer strand might be identified via the characteristics of the blockage current, but this hope may be unrealized because of first-principle signal-to-noise limitations and because the naturally occurring nanopore is thick enough that several monomers of the biopolymer are present in the nanopore simultaneously.
More recent research has focused on fabricating artificial nanopores. Ion beam sculpting using a diffuse beam of low-energy argon ions has been used to fabricate nanopores in thin insulating substrates of materials such as silicon nitride (See Li et al., “Ion beam sculpting at nanometer length scales”, Nature, 412: 166-169, 2001). Double-stranded DNA (dsDNA) has been passed through these artificial nanopores in a manner similar to that used to pass ssDNA through naturally occurring nanopores. Current blockage data obtained with dsDNA is reminiscent of ionic current blockages observed when ssDNA is translocated through the channel formed by α-hemolysin in a edgeid bilayer. The duration of these blockages is been on the millisecond scale and current reductions have been to 88% of the open-pore value. This is commensurate with translocation of a rod-like molecule whose cross-sectional area is 3-4 nm2 (See Li et al., “Ion beam sculpting at nanometer length scales”, Nature, 412: 166-169, 2001). However, as is the case with single-stranded biopolymers passing through naturally occurring nanopores, first-principle signal-to-noise considerations make it difficult or impossible to obtain information on the individual monomers in the biopolymer.
A second approach has been suggested for detecting a biopolymer translocating a nanopore in a rigid substrate material such as Si3N4. This approach entails placing two tunneling electrodes at the periphery of one end of the nanopore and monitoring tunneling current from one electrode, across the biopolymer, to the other electrode. However, it is well known that the tunneling current has an exponential dependence upon the height and width of the quantum mechanical potential barrier to the tunneling process. This dependence implies an extreme sensitivity to the precise location in the nanopore of the translocating molecule. Both steric attributes and physical proximity to the tunneling electrode could cause changes in the magnitude of the tunneling current which would be far in excess of the innate differences expected between different monomers under ideal conditions. For this reason, it is difficult to expect this simple tunneling configuration to provide the specificity required to perform biopolymer sequencing.
Resonant tunneling effects have been employed in various semiconductor devices including diodes and transistors. For instance, U.S. Pat. No. 5,504,347, Javanovic, et al., discloses a lateral tunneling diode having gated electrodes aligned with a tunneling barrier. The band structures for a resonant tunneling diode are described wherein a quantum dot is situated between two conductors, with symmetrical quantum barriers on either side of the quantum dot. The resonant tunneling diode may be biased at a voltage level whereby an energy level in the quantum dot matches the conduction band energy in one of the conductors. In this situation the tunneling current between the two conductors versus applied voltage is at a local maximum. At some other bias voltage level, no energy level in the quantum dot matches the conduction band energy in either of the conductors and the current versus applied voltage is at a local minimum. The resonant tunneling diode structure can thus be used to sense the band structure of energy levels within the quantum dot via the method of applying different voltage biases and sensing the resulting current levels at each of the different voltage biases. The different applied voltage biases can form a continuous sweep of voltage levels, and the sensed resulting current levels can form a continuous sweep of current levels. The slope of the current versus voltage can in some cases be negative. Conceptually, it is also possible to inject a known current between the conductors and measure the resulting voltage, but this approach can fail if the characteristic current versus voltage has a negative slope region. For this reason, applying a known voltage bias and sensing the resultant current is usually the preferred method.
As discussed in Nonprovisional application Ser. No. 10/352,675 referenced above, a resonant tunneling electrode arrangement can be associated with a nanopore so as to sense the presence, and energy band properties of, a biopolymer molecule extending through the nanopore. This resonant tunneling electrode arrangement provides hope of not only sensing or characterizing a biopolymer, but of identifying the constituents of the polymer and meeting the goal of rapid and efficient DNA sequencing.
Thus there is a need for specific resonant tunneling electrode structures to be associated in such an arrangement with the nanopore in order to characterize biopolymers such as DNA, a method of using such resonant tunneling electrode structures to characterize biopolymers, and methods of building such resonant tunneling electrode structures. The references cited in this application infra and supra, are hereby incorporated in this application by reference. However, cited references or art are not admitted to be prior art to this application.